Making this a mod is not to difficult it will just take a little time < 1 hr.
1) Download the latest Forge Tools
2) Unzip the tools rar file
3) Locate the \ForgeTools1.1\ReferenceData\GameInfo folder and inspect the entity files you want to modify for your mod.
4) Create a folder that you want your mod to be called and copy the GameInfo folder to the mod path on your computer. I have xp it should be something like: C:\Documents and Settings\[computername]\Local Settings\Application Data\Ironclad Games\Sins of a Solar Empire\Mods\My autofleet mod\
5) Open up FrigatePhaseScout.entity file for example. Notice the 6th line autoJoinFleetDefault variable is set to false. This is what needs to be changed for each of the games ships that you want to not have autoJoinFleetDefault set to.
6) Any of the entity files with Phase = Vasari, Psi = Advent, Tech = Tec.
7) Change any of the ships you want.
8) The documents folder where you unziped the Forge tools has a good example of making a simple mod.